# Differentially Methylated Regions Caller

## Documentation for package ‘DMRcaller’ version 1.43.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

DMRcaller-package | Call Differentially Methylated Regions (DMRs) between two samples
analyseReadsInsideRegionsForCondition | Analyse reads inside regions for condition
analyseReadsInsideRegionsForConditionPMD | Analyse reads inside regions for condition
computeCoMethylatedPositions | Compute pairwise co-methylation statistics for cytosine sites within regions
computeCoMethylatedRegions | Compute pairwise co-methylation statistics between regions
computeDMRs | Compute DMRs
computeDMRsReplicates | Compute DMRs
computeMethylationDataCoverage | Compute methylation data coverage
computeMethylationDataSpatialCorrelation | Compute methylation data spatial correlation
computeMethylationProfile | Compute methylation profile
computeOverlapProfile | Compute Overlaps Profile
computePMDs | Compute PMDs
computeVMDs | Compute VMDs
DMRcaller | Call Differentially Methylated Regions (DMRs) between two samples
DMRsNoiseFilterCG | The DMRs between WT and met1-3 in CG context
extractGC | Extract GC
filterDMRs | Filter DMRs
filterPMDs | Filter PMDs
filterVMDs | Filter VMDs
filterVMRsONT | Filter VMRs for ONT Data
GEs | The genetic elements data
GEs_hg38 | The genetic elements data of GRCh38 Genome Reference
getWholeChromosomes | Get whole chromosomes from methylation data
joinReplicates | Joins together two GRange objects in a single containing all the replicates
mergeDMRsIteratively | Merge DMRs iteratively
mergePMDsIteratively | Merge PMDs iteratively
methylationDataList | The methylation data list
ontSampleGRangesList | The ONT methylation data list
ont_gr_GM18870_chr1_PMD_bins_1k | Partially Methilated Domains example
ont_gr_GM18870_chr1_sorted_bins_1k | The ONT methylation data example
plotLocalMethylationProfile | Plot local methylation profile
plotMethylationDataCoverage | Plot methylation data coverage
plotMethylationDataSpatialCorrelation | Plot methylation data spatial correlation
plotMethylationProfile | Plot Methylation Profile
plotMethylationProfileFromData | Plot methylation profile from data
plotOverlapProfile | Plot overlap profile
PMDsBinsCG | The PMDs between GM18501 and GM18876 using Bins method
PMDsNoiseFilterCG | The PMDs between GM18501 and GM18876 using Noise_filter method
poolMethylationDatasets | Pool methylation data
poolTwoMethylationDatasets | Pool two methylation datasets
readBismark | Read Bismark
readBismarkPool | Read Bismark pool
readONTbam | Load ONT BAM, decode MM/ML, and count modified vs. unmodified reads
saveBismark | Save Bismark
scanBamChr1Random5 | The bam file from ONT nanopore .pod5 files
selectCytosine | Select Cytosine Positions
syntheticDataReplicates | Simulated data for biological replicates